SharePoint Site Collection Administrator – the user responsible for the entire site collection, has access to Site Collection wide features in several places including Site Settings, typically is the person responsible for a department or a group’s entire site collection.

SharePoint Site Owner – a user with “full control” rights to a single site, it’s lists, libraries and content, and any sub sites and workspaces created below it. I.e. responsible for a “branch” of a site collection.

Here's a list of what the Site Collection Administrator can see that the Site Owner (Full Control user) can not:

Site Actions -> Site Settings

-- Users and Permissions---- Site collection administrators (only an option when at a top level site)

-- Galleries---- Workflows

-- Site Administration---- Content and structure logs

-- The entire Site Collection Administration column is missing(which also means that the full control user can't access the 2nd level Recycle Bin)

And interestingly enough... we don't trust the Full Control user with all of these features, but they can delete the site!

Here’s the Site Actions –> Site Settings screens…

For the Site Collection Administrator, at a top level site:

(Circled items are not available to the Site Owner)

For the Site Owner, at a top level site:

For the Site Owner, at a sub site you will be missing “Save site as template” and many of the Galleries items:

For sub sites both the Site Collection Administrator and the Site Owner the Galleries column is reduced to these choices.

Also, the “Site collection administrators” link is only available at the top level site.